Stefan: yes, so I checked out and built the latest from github:
./jython
Jython 2.7.1b3 (, Jan 19 2017, 11:18:13)
[Java HotSpot(TM) 64-Bit Server VM (Oracle Corporation)] on java1.8.0_112
Type "help", "copyright", "credits" or "license" for more information.
Unfortunately the problem is still there for me. Note that I have a full history in the ~/.jline-jython.history file - it's 500 entries.
When I cut the history file down to either 50 or 400 then it works fine for retrieving all items. So it seems like it may be an edge case?
In fact, further testing seems to indicate that things only start to be problematic once the history size hits the maximum. After that, when trying to read entries in the lower range (from 1) you start to see exceptions.
Hope that helps.